In this paper, we present a new approach to reconstruct dipole magnitudes of a distributed source model for magnetoencephalographic (MEG) and electroencephalographic (EEG). This approach is based on the structural homogeneity of the cortical regions which are obtained using diffusion MRI (dMRI). First, we parcellate the cortical surface into functional regions using structural information. Then, we use a weighting matrix that relates the dipoles' magnitudes of sources inside these functional regions. The weights are based on the region's structural homogeneity. Results of the simulated and real MEG measurement are presented and compared to classical source reconstruction methods.